API for ndukler/phyloGLM
Tests for signals of variable rates of evolution between gene classes and lineages for probabalistic alleles
| Global functions | |
|---|---|
| alleleData | Man page Source code |
| alleleData-class | Man page |
| alleleDataValidityCheck | Source code |
| bic | Man page |
| copy | Man page |
| disCharToProb | Man page Source code |
| expokit_dgpadm | Source code |
| fit | Man page |
| forceParameterZero | Man page |
| getAlleleData | Man page |
| getEdgeTable | Man page |
| getEdgeTable,alleleData,alleleData-method | Man page |
| getEdgeTable,rateModel,rateModel-method | Man page |
| getParams | Man page |
| getParams,rateModel,rateModel-method | Man page |
| getRateBounds | Man page |
| getRateBounds,rateModel,rateModel-method | Man page |
| getSiblings | Man page Source code |
| getSiteInfo | Man page |
| getSiteInfo,alleleData,alleleData-method | Man page |
| getSiteInfo,rateModel,rateModel-method | Man page |
| getTree | Man page |
| ll | Man page |
| logSumExp | Man page Source code |
| lrt | Man page |
| marginal | Man page |
| marginalTransitions | Man page |
| matrixToStlXptr | Man page Source code |
| pack | Man page |
| packedModel-class | Man page |
| phyloGLM | Man page |
| phyloGLM-package | Man page |
| phyloGrad | Man page |
| phyloHess | Man page |
| pi | Man page |
| plotElementTransitions | Man page |
| plotElementTransitions,rateModel,rateModel-method | Man page |
| plotParams | Man page |
| plotParams,data.frame,data.frame-method | Man page |
| plotParams,rateModel,rateModel-method | Man page |
| plotTree | Man page |
| plotTree,rateModel,rateModel-method | Man page |
| predict | Man page |
| rateModel | Man page Source code |
| rateModel-class | Man page |
| rateModelValidityCheck | Source code |
| rates | Man page |
| readPAF | Man page Source code |
| scaledLL | Man page |
| se | Man page |
| se,rateModel,rateModel-method | Man page |
| setFixed | Man page |
| setParams | Man page |
| setParams,rateModel,rateModel-method | Man page |
| setRateBounds | Man page |
| setRateBounds,rateModel,rateModel-method | Man page |
| show | Man page |
| simulateSites | Man page Source code |
| siteLL | Man page |
| siteLL,rateModel,rateModel-method | Man page |
| stlMatrix | Man page Source code |
| stlMatrix-class | Man page |
| stlMatrixSubset | Source code |
| unpack | Man page |
| updateFixed | Man page Source code |
| updateFormula | Man page |
